When Cavil leaves Ellen and Boomer alone to talk, Ellen offers Boomer an apple. This is a likely reference to the Book of Genesis in The Bible and the "fruit" from the tree of knowledge of good and evil. Satan convinced Eve to eat the fruit of the tree. Eve in turn convinced Adam to eat the fruit.
Cavil could be taking on the role of Satan, with Ellen as Eve. It should be pointed out that the Biblical text never mentions an apple but most people think of the fruit of the tree of knowledge as an apple.
Furthermore, the consumption of the fruit is often thought of as a metaphor for sexual relations, that Eve had intercourse with Satan. Likewise, Ellen had engaged in sexual intercourse with Cavil in a previous episode, although the parallels get confused in terms of the creator-creation relationship between Cavil and Ellen.
Ellen was trying to get Boomer to realize the difference between her philosophy and that of Cavil, and then to choose a side. That could be a more literal take on the idea of the apple representing knowledge of "good" and "evil".